I would couple it with the membrane to be honest. The point of the different groups is to avoid the hot solvent cold solute sitution. Molecules with similar degrees of freedom have comparable heat capacities. Your small peptide is closer in size and bond layout to a lipid chain than to water. The end state of the system also hase the peptide physically coupled to the bilayer too, so Membrane_Peptide seems to be most consistent approach.
On 2012-10-11 07:23:26PM -0700, fciocco wrote: > Hi > > I have a system with a lipid bilayer (128 phospolipids), aproximately 30 SOL > molecules per lipid, and a small highly charged peptide at certain distance > from the bilayer. I want to do a pulling simulation in order to pull the > peptide inside the membrane along the z-direction. So, taking into account > that I want to explore the differents configurations doing a serie of US > simulations, and that in some windows I have the peptide in the water bulk > and in others it is inside the hydrophobic core of the membrane (but with > some hydration water molecules), I'm wondering about what is the best > approach for define the tc-groups..? > Peptide Membrane SOL_Ions or Membrane Peptide_SOL_Ions ? > > Note: when I choose the peptide separately, the temperature fluctuations are > high (between 50 and 100K approximately). > > any comment would be very appreciated. > > best regards, Facundo > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/small-tc-group-tp5001927.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
